BSDB

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN I J |I-J| Displacement error 1 1 7 6 140.32 3.33 2 4 7 3 233.84 1.14 3 4 10 6 192.69 4.12 4 5 50 45 67.93 0.10 5 5 53 48 66.02 0.18 6 6 9 3 244.57 0.98 7 6 46 40 73.27 2.35 8 6 47 41 70.50 1.34 9 6 50 44 70.42 1.31 10 6 54 48 66.15 0.14 11 7 10 3 241.12 1.41 12 8 12 4 239.29 0.49 13 8 43 35 83.78 0.58 14 8 46 38 83.70 0.61 15 9 12 3 241.12 0.71 16 9 15 6 205.75 0.37 17 9 43 34 83.83 0.59 18 9 47 38 83.67 0.62 19 9 54 45 82.39 0.73 20 10 15 5 232.65 1.99 21 11 15 4 232.66 1.99 22 11 16 5 232.65 1.99 23 12 15 3 235.44 0.59 24 12 16 4 234.19 1.24 25 13 16 3 241.82 0.96 26 13 17 4 237.43 1.25 27 14 17 3 238.09 0.92 28 14 18 4 235.80 0.43 29 14 39 25 92.41 2.19 30 15 18 3 238.83 1.28 31 15 19 4 237.42 1.26 32 15 57 42 83.50 0.49 33 16 20 4 239.99 0.03 34 16 62 46 57.45 2.67 35 17 20 3 242.50 1.23 36 17 21 4 240.23 0.10 37 18 21 3 243.11 1.34 38 18 22 4 240.23 0.10 39 18 32 14 100.41 1.81 40 18 36 18 97.36 0.28 41 19 22 3 240.23 0.10 42 19 23 4 240.21 0.10 43 19 57 38 84.00 0.58 44 19 58 39 83.70 0.46 45 19 60 41 83.67 0.46 46 19 62 43 76.50 2.34 47 20 23 3 240.19 0.12 48 20 24 4 240.31 0.06 49 20 62 42 79.36 0.92 50 21 24 3 241.44 0.17 51 21 25 4 231.69 0.50 52 21 28 7 189.85 6.24 53 22 25 3 235.28 2.46 54 22 26 4 214.50 0.93 55 22 28 6 178.02 0.33 56 22 29 7 145.85 2.65 57 22 32 10 143.02 1.37 58 22 58 36 84.02 0.58 59 23 58 35 84.06 0.56 60 23 59 36 83.87 0.54 61 23 60 37 83.73 0.47 62 25 28 3 242.90 0.44 63 26 29 3 248.61 3.29 64 26 30 4 251.67 1.76 65 27 30 3 264.38 0.07 66 28 31 3 237.86 0.27 67 28 32 4 233.74 1.33 68 29 32 3 235.63 0.84 69 29 33 4 230.05 1.95 70 29 54 25 96.02 0.85 71 29 55 26 95.86 0.80 72 29 58 29 90.90 2.39 73 30 33 3 233.75 0.10 74 30 34 4 230.05 1.95 75 31 34 3 232.25 2.68 76 31 35 4 231.35 2.60 77 32 35 3 234.53 1.01 78 32 36 4 231.34 2.60 79 32 58 26 88.81 0.18 80 33 36 3 237.56 0.01 81 33 37 4 235.63 0.46 82 33 44 11 134.56 0.89 83 33 47 14 134.56 0.89 84 33 51 18 123.15 1.84 85 33 54 21 100.18 0.52 86 34 37 3 235.95 0.30 87 34 38 4 235.63 0.46 88 35 38 3 243.42 3.21 89 35 39 4 243.42 3.21 90 36 39 3 244.53 2.66 91 36 40 4 222.72 1.28 92 36 41 5 217.72 3.79 93 36 43 7 184.36 4.95 94 36 44 8 141.54 3.88 95 36 47 11 149.50 0.12 96 37 41 4 173.72 1.67 97 37 44 7 159.59 5.38 98 40 43 3 231.93 0.49 99 40 44 4 229.06 1.93 100 41 44 3 231.94 0.49 101 41 45 4 229.06 1.93 102 42 45 3 245.77 1.06 103 42 46 4 236.03 1.56 104 43 46 3 237.23 0.97 105 43 47 4 236.03 1.57 106 44 47 3 236.66 1.27 107 44 48 4 235.96 1.62 108 45 48 3 237.12 1.04 109 45 49 4 233.39 2.90 110 46 49 3 236.93 1.14 111 46 50 4 233.40 2.90 112 47 50 3 238.81 1.74 113 47 51 4 224.05 0.48 114 47 54 7 191.83 7.37 115 48 51 3 234.94 3.67 116 50 53 3 242.56 0.14 117 50 54 4 233.13 1.93 118 51 54 3 239.66 1.31 119 51 55 4 233.13 1.93 120 52 55 3 241.91 0.46 121 52 56 4 241.90 0.46 122 53 56 3 241.91 0.46 123 53 57 4 241.90 0.46 124 54 57 3 242.59 0.80 125 54 58 4 233.61 4.61 126 55 58 3 235.83 3.48 127 55 59 4 233.53 4.63 128 56 60 4 233.79 4.50 129 57 60 3 245.70 0.35 130 64 67 3 242.37 0.71 131 65 68 3 248.05 0.82 132 66 69 3 245.72 1.54 133 66 70 4 170.54 4.50